Downloading the Gene level Copy number files from TCGA, I computed CIN in the following way: - gene CNV > 2.25 = Amp - gene CNV < 1.75 = Del
I have mapped cytobands to gene entrez ids using org.Hs.egMAP and using the cytobands I extract the gene level CIN which will be added at cytoband level for all the genes in that cytoband across all the different cases that we have from TCGA-SARC
Plots: 1- Overall boxplots: for each chromosome all the cytoband CIN per sarcoma type
1b - Overall heatmap: for each chromosome a heatmap with all the CIN per cytobands and annotation on the side for each sarcoma type
2- HRD boxplots: The same as before but separating HRDhigh/low
2b - is there any cytoband differentially expressed between HRD/low groups in particular?
3- Make enrichment in those cytobands :)
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## OUTPUT:
## Number of Chromosome sets: 1
## Number of Chromosomes in set 1 : 2
## Processing data..
## Number of annotations in data set 1 : 9547
## Visualizing..
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## OUTPUT:
## Number of Chromosome sets: 1
## Number of Chromosomes in set 1 : 2
## Processing data..
## Number of annotations in data set 1 : 9547
## Visualizing..
Copyright © 2022 Alicia Pliego. FTP lab. All rights reserved.